Doctor Whooves: Princess Twilight
by The Idealist 33
Summary: One hundred years after the marriage of Twilight Sparkle and Flash Sentry, Twilight is found visiting the graves of her old friends including Flash Sentry's, when she receives a letter from a group of ponies she hoped never to hear from again. How will Twilight get out of this mess? Will she have to do it alone? Or will she make new friends along the way?
1. Twilight

Doctor Whooves: Princess Twilight

**T**wilight

Twilight was sitting down looking at a tombstone. She looked serious as she read the name on it but then smiled as she pulled some flowers out and placed them on the ground. "Happy 100th anniversary Flash. I'll never forget you," she said as a tear rolled down her eye.

She then walked around as she put her hoof on his stone and went to go look for another tombstone. She trotted along and found AppleJack's. It had her cutie mark on it, as most of the tombstones did, and the word honesty written at the bottom. She walked past it as she left a small flower on the floor of hers too. She continued on and found Pinkie Pie's and did the same. She walked around the cemetery doing it to all of her old friends until she reached Rarity's and put the flower there too. Sweetie Bells was right next to Rarity's. She turned around and smiled as more tears rolled down her cheeks. "I love you guys. If it wasn't for you guys the whole world would be in chaos."

After a few minutes she made her way to leave but then saw a young white pony, probably a teen, walking into the cemetery. "Twilight? Princess Twilight!?" she called out.

Twilight got a closer look at her and saw that it was Rarity's granddaughter, "Jewel Gem?" she said smiling as she flew up towards the young pony.

"I haven't seen you in such a long time!" she told the princess. Ever since you moved out of Ponyville things haven't been the same."

"Yeah, but at least things have been quiet for a couple of year," she said hugging her.

Jewel hugged back, "Why are you here? Wanted to see the old team again?"

"Heh, actually it's mine and Flash Sentry's 100th anniversary," she said as she looked at his grave again.

"Aww that's nice. I just wanted to see my grandparents."

"That's good. I still never would have expected Rarity to get married like that. Oh well. Thanks to her you were born."

"Thank you. Are you going to stay?"

"I'm sorry, but I wasn't even supposed to be her. I have to get back to my kingdom."

"Okay. Goodbye Princess Sparkle."

She smiled, "You can call me Twilight. I'll try to visit as much as I can," Twilight said as she flew up. Jewel Gem waved as she flew away. Twilight arrived at the train station and waited to be seated. She started crying again, but tears of joy. She took it hard at first as her friends started aging faster than she was but after a few years to deal with their passing she realized that death is a natural part of life. Celestia, Luna, and Discord helped her with that. The conductor called all the ponies in and she trotted too her seat.

Right as she sat down a scroll appeared in front of her. "Ugh, what is it now Spike?" she said as she opened it expecting another letter asking her where the ingredients for some potions were. It would have been the 5th time since she got on the train, but it wasn't. It was from someone she had hoped she would never hear from again.

…

Deep on the outskirts of the crystal empire a dark flash escaped the ground. It was magical but evil at the same time. Just as it seemed like nothing else would happen a hoof rose out of the dirt. A second one rose up and then a big figure rose up out of the darkening earth, panting quickly to catch his breathe. "AHHH!"

He pulled himself out, his horn glowing brightly, which was ironic because it was dark magic, then suddenly turning off. "I…I'm finally…back…" he said as she tried to stand up but his weak legs gave out and he fell head first into the hard ground.

He tried to get up again and succeeded this time but he still felt really weak. Even his cape looked like it needed to take it easy for a few weeks. He tried to use his magic but he felt absolutely nothing, "Buck! After more than a hundred years trying to reform myself, I think I have run out of magic!" he said as he looked around and saw the crystal empire.

He squinted at it and through, "Those crystal ponies. The once great empire! Once lead by the greatest pony of all time! BY ME!" Sombra yelled. Suddenly he felt a sharp pain in his neck and tried to turn around to see what it was but before he could he was out cold. The only thing he could make out was out line of five ponies.

…

"Dear Twilight:

For weeks now we have discovered a disturbance on the outskirts of the crystal empire. We wanted to inform Princess Cadence and Prince Shining Armour, but decided to figure out what it was before we stirred up any trouble as you know we usually do. As we started studying the source we discovered that there was very powerful magic working underneath the ground. We were able to trace an outline of the magic that looked almost like a pony. This morning we saw that it was becoming denser and arrived just in time as we found the body of an old enemy of yours. King Sombra. Please contact us ASAP.

Sincerely: TORCH WOOD


	2. Wrath

**And a rather long chapter after a few weeks. Sorry working on the SAT crap but once it's over be prepared for lots more chapters! Enjoy the return of an old friend!**

**W**rath

In the Torch Wood tower in the center of Coltiff England, five ponies were working on their own little things. Maybe not little. It was all about Sombra. An Asian looking female was working on one of the computers. They have just come out with them not 5 years ago and they had made things so much easier for Torch Wood after over a 100 years of their research in alien activities. Two of them were down in the dungeon watching over Sombra who was in a magic proof cell. The female looked quite young and beautiful. White fur and pink hair, but don't confuse her for her looks, she is quite deadly when she needs to be. She was the youngest of the group. The male was probably ten years older than her had green fur, was bald and had a small scar near his chin. He was the teams' doctor and was studying Sombra to see how he could have possibly lived after 100 years of the Crystal Empire being awakened.

Another one of the ponies was talking to the teams' leader, "Sir, This doesn't make any sense. Even somepony like you must know that this is impossible."

"It's possible, because he's right there. I haven't dealt with this pony in over a thousand years," he said looking at the security cameras down in the dungeon just in case anything went wrong.

The pony known as Odd, average sized pony with blue fur and purple hair said to him, "Well he did create you"

Captain Jack Horesness stepped out of his chair. He looked exactly as he did 100 years ago. Heck he looked exactly the same as he did a 1000 years ago! "Yeah, and I don't think he's going to appreciate me being on the good guys team now."

"Jack?" he heard a voice over the communication device in his ear. "Permission to go in?" the doctor asked. His name was McGann, but the team always made fun of him and called him Megan.

"Sure, go ahead Yumi," Jack told the pony that was working in the computer.

"Sure thing," she said as she unlocked the doors. She was a Pegasus, had purple fur and dark purple hair (dyed), and used black eye liner.

As the door opened Kat asked McGann, "Are you sure you want to do this?"

"I can't study him from behind these glass walls," he said walking in and then the door locked behind him. He walked up to Sombra who was in a strait jacket still passed out. He pulled up a small device, "Hm, no magic detected in this room except for me. Something must have happened when he was reforming himself." He brought the device closer to his horn, still nothing. "I don't think he's dangerous," he told Kat through the wall.

Suddenly, Sombra's eyes opened up. "AAHHH!" he yelled as he quickly stood up on his back legs and rammed into McGann, slamming him into the wall. "Who are you!? You little ponies will pay for placed King Sombra in this cell!" he said about to use his magic on the doctor, but nothing happened.

McGann stared at him. His back hurt from being rammed but he was far more intrigued that a pony as powerful as Princess Celestia could just 'run out' of magic. "Intriguing! Maybe it was your retransformation. You must have used a boat load of magic to recreate your body!"

"What? What are you talking about?! You're insane!" he said trying to use his magic on him again, but he felt nothing! "Work! Work! Work!" he yelled even hitting his head on the wall. "No! Without my magic I'm nothing! Give it back you stupid pony!" he said placing his horn on McGann's neck. "NOW!"

The door opened and Kat was pointing a gun at Sombra, "That's enough! Let the stallion go right now!"

Sombra backed up, "Fine! Then leave me alone!" he said getting back on his bed. "I don't see why you keep a common household earth pony locked up in a magic proof cell."

"You're magic could come back at any moment," McGann said standing up.

"Shut up. If I had my magic you would have run away screaming like a little girl when I first opened my eyes."

"I don't fear easily," he said actually walking up to Sombra. "I'm here to help you. Find out what's wrong with you."

"Why would you want to help me? I enslaved an entire empire."

"That was over 1,100 years ago. Now without your magic you might have a different view on things."

"Oh I see! You are the idealistic one aren't you!" he said sitting up. "You know what old saying about how someponies can change? Well the whole saying goes, 'Someponies change, most ponies don't.'"

McGann walked up to Sombra and Kat got worried and aimed her gun at Sombra's chest, "What are you doing?"

He used his magic to take of Sombra's strait jacket. Sombra just looked at him with discust, "You being nice won't save anypony," he kissed.

"No, but I want you to be comfortable for when Princess Twilight shows up," he said smiling as he walked out the door with Kat and then locked the door.

"Wait what!? No! Don't bring her here! She would kill me after what I did to her brother and sister in law! GET BACK HERE!"

"Well I think you finally got to him," Kat said walking with him upstairs.

They heard Jack over their com-links, "Alright guys. Princess Twilight and the Queen are going to be here very shortly."

"Wait, Director Luna is coming too?" Yumi asked.

"Yes, she must be very interested in this if she is personally come down here herself."

Odd spoke, "She hasn't been down here in years. She usually only cares when we pick up time rifts around Equestria."

"Ha, you know exactly who she's looking for," Kat said.

Jack answered back, "Oh come on give her a break."

"And we all know why Jack wants to keep track of the time rifts. A certain 'Doctor,'" McGann said.

"Alright Megan! What me and Luna do is none of your business!" Jack yelled at them.

"He's just upset about how he got left behind after Spitfi…" Yumi was interrupted.

"Okay! That's enough! That day still haunts me okay! I just wanna forget it!" he said growing impatient.

"If you want to forget it so badly why are you still obsessed with the Doctor then?" McGann said.

Before Jack could answer again the intercom said, "Recognized, 0-1 Queen Luna arriving now."

"Crap. Okay everypony get to the entrance," Jack said leaving the conference room with Odd.

The big round door opened and Luna (looking the same as always) arrived with her head held high. "Your majesty," they all said bowing.

"Greetings fellow Torch Wood members. I hear you have literally buried up an old foe."

"Yes queen. The strange thing though is that he has no more magic. At least for the moment," Jack said.

McGann then answered, "If I had to guess I believe it's because of the large amount of magic it took to reform him, but I still don't get how he did it."

"Hm," Luna said thinking, "If his horn would have survived the blast then it could have easily started working on remaking his body, but even that still requires a lot of magic and more than just a 100 years."

"If you want to see him…" Jack started but was interrupted when they heard "Recognized, 0-4 Princess Twilight arriving now."

Twilight came storming in as the door opened, "Where is he!? He will pay for all the damage that he had caused a hundred years ago!"

"Princess Twilight, please calm down," McGann said. "He don't have any magic. He's defenseless. You going in there and beating the buck out of him wouldn't be a good image for the Princess."

"Ugh, fine, but I will see him! With or without you guys."

McGann turned to look at Jack and he nodded, "Okay, right this way," he said leading them all downstairs to where the cells were. They had 3 of the cells full. One obviously had Sombra. Another one had a yellow looking pony…thing who was running in circles in his cell with super speed. The weird thing about that pony thing was that he had no eyes, no mouth, no ears, no nose, no mane or even a tail. In the other cell was a really old foe, Tirek.

When they arrived at Sombra's cell he was facing them. Almost as if he had been waiting for them. "So Twilight really is here," he said.

"THAT'S PRINCESS TWILIGHT TO YOU!" Twilight yelled at him.

He backed up a bit but then leaned towards her, "Hm, wings. You really are a princess. Well I guess you do reserve the respect 'Princess Twilight.'"

"You bet I do! Especially from you! You were trying to enslave an entire kingdom!"

"Well it was either that or kill them all. I guess you could say I chose the best path."

"You didn't have to do anything with those poor ponies! You could have just left them alone you monster!"

He sighed, "All of those with power are afraid to lose it, but I've already lost my kingdom and my magic. I have nothing left to lose. I never had any friends. Nothing!"

Twilight tried to zap him with magic but since the cell was enchanted it backfired and she quickly ducked as it hit the wall behind them.

"Hehe, you have nothing to threaten me with!" he yelled at her.

"ENOUGH!" Luna yelled at both Twilight and Sombra before they both tried to kill each other. "Twilight! I want you to take Sombra under your wing. Make friends with him just as Celestia did with Fluttershy and Discord all of those years ago."

"WHAT!?" both Twilight and Sombra yelled and looked at her. "YOU CAN"T BE SERIOUS!" they both said yet again.

"I am, and Twilight, if anything goes wrong you may use your magic against Sombra."

"Ha!" Twilight said to Sombra.

"But just to make sure you don't unless absolutely necessary I will take your wings and your high honor away."

"WHAT!?" Twilight yelled. "What if he tries to kill me!?"

"Then use your magic, but I will still take it all away until I see fit to give it back to you. I know if anything bad were to happen that you will value the safety of everypony more than your title."

"Mhh, fine!" Twilight said but she was obviously still mad.

"Okay good. Jack release Sombra." Jack nodded to her then to Yumi. Yumi walked out.

"What!? Already!? He could just be hiding his magic and getting ready to kill me!" Twilight said.

"Oh don't worry. I scanned him myself. There's no way he has magic right now," McGann said.

"Ugh! I hate you all!" she said storming out of the dungeon. The door to Sombra's cell opened up right after she left.

All the team had their guns ready just in case except for Luna and McGann. "Pull any funny moves and we will kill you," Jack said taking out his gun.

"Oh puh-lease. Like you could really kill the King of Darkness."

Jack smiled, "No, but the Queen of Darkness might."

Sombra looked and Luna, "So she's a queen now? Who's the lucky stallion?"

Luna just looked at him with cold dead eyes, "If you so much as even hurt Twilight, I will kill you."

He swallowed, "Understood."

They suddenly heard a beeping sound and everybody went upstairs, "Move Sombra!" Odd said pulling Sombra up with the rest of the team.

"What is it Yumi?" Jack said walking up to where she was seating. Twilight was right behind her.

"Both of you two are going to like this. Time rifts."

"What!?" Queen Luna and Jack said. "Where!? How big!?"

"Whoa calm down you two. There is one big one. Really big one."

"The Doctor!" Jack said. "Where!?"

"A couple of blocks from here and there is also a small rift not too far from that!"

"I.D.!" Luna yelled. "I have to go get him!" She quickly disappeared before Yumi could protest.

"I have to go find the Doctor!" Jack said heading towards the door.

"Wait! There is a third one too! Medium sized!"

"Wait what?" he said turning around.

"Right between them. I don't get what it could be."

Sombra recalled something and turned away. "It couldn't be. Are you guys talking about time travel?"

Twilight looked at him suspiciously, "Yes, what do you know about it?"

"Um…nothing. Are we going to go see what it is?"

"I have to!" Jack said heading out and running towards the sources of the time rifts.

"Let's go," McGann said as he grabbed his gun.

Luna obviously got there first and saw the TARDIS, ID and a weird looking red oval shaped device, but she didn't care. She ran quickly towards ID who was passed out on the sidewalk. "ID!"

She picked him up and he moaned. She quickly teleported back into the HQ. She arrived just as the team was headed out, "McGann! I need your help!"

"Alright everypony go with Jack I'll stay here and help ID."

"He must have been working with the Doctor and something must have gone wrong," she said placing him on the table.

McGann quickly checked him over, "I think he just passed out for a moment. Too much time travel I'm guessing."

"Yeah, he tends to do that," she said with some tears in her eyes.

McGann noticed but didn't say anything about it, "He's gonna be alright."

"Okay. Thank you."

Jack came in right after with a very familiar grey pony with a bow tie, but he was also passed out. "McGann! Check him out! Make sure he's alright! I'm pretty sure he has a heart beat but I don't know for sure!"

"So this is the famous doctor hu?" he said looking him over, "Wow, he does have 2 hearts! He should be fine. I can't find anything wrong with him either."

The top of their base opened up and the red oval shape…timey wimey thing came in along with the rest of the team. "We brought the machine sir. Do you even have any idea what it is?"

"No, but bring the TARDIS down here too. We will figure out what happened with ID and the Doctor when they wake up."

"Don't do anything to them. Okay?" Luna said seeing ID's time manipulator beeping.

"Are you sure?" Jack said. "We can at least see where they were last, or at least where ID was last."

"No, just leave them."

Sombra was staring at them all from the side, but mostly at the time machines. "That son of a bitch actually did it."

"Did what!?" Twilight said from behind him. He had no idea he was standing behind him.

"Oh um, nothing!"

"Do you know something about the Doctor?" she said getting closer to him. Even though he was taller, bigger, and stronger he was afraid of her.

"No. I've never heard of him."

"So you know something about the red machine then?"

He sighed, "Maybe. I don't know! I knew a pony that was always talking about time travel and asked me to help him. I used to be a scientists pony. And a scientists experiment also."

"Yeah, I've heard. I'll agree it was unfair but it's still your fault. You didn't have to kill all those ponies in the hospital."

"It wasn't my fault. I felt, strange. Bursting with power! I couldn't control it, and when I actually did kill somepony I could sense the blood! Delicious blood! I needed energy! More power!"

"Hm…so could drinking blood get you your powers back?" she asked.

"I have no idea."

Twilight didn't like that. Who would stop him from breaking free and drinking ponies' blood? 'I should tell the queen.'

Sombra didn't need mind reading powers to know what she was thinking about, but before anymore happened ID woke up.

"Ah! Who! What!? Where!? Luna!" he said hugging her. "Oh my goodness! It's been days since I last saw you!"

She pushed him back with a smile on her face, but then she slapped him, "IT'S BEEN TWO YEARS FOR ME!"

"Ouch! What!? No it should have been just one month! Something must have gone wrong! Wait! Why am I here?"

Jack came up, "We found you passed out on the sidewalk along with the TARDIS and that!" he said pointing to the other machine.

"What's that?" he said looking at the device. "I've never seen that thing before in my life! And I certainly would have remembered if I would have been traveling with the TARDIS!"

"Wait," Odd said, "you have no idea why all three of you appeared here at the same time?"

"No, I was just traveling back to Equestria because I wanted to see Luna but…all I remember is hitting the coordinates and then waking up here!" then he thought about it, 'Wait…I remember a red and blue light,' but since he didn't say it out loud only Luna heard him.

As they all talked Sombra and Twilight stayed in the back. They had nothing to do with this team so he didn't think they should be a part of it. Sombra kept looking at the red oval and saw a bunch of weird curves that might have been door handles or at least some way to get inside. "I want a closer look at that," he said walking back Twilight to the machine.

"Don't touch it," she said walking with him. "Don't even stair at it for too long. You could go blind."

"Ha! I have superpony hearing. I could walk through a maze with my eyes close."

"Still! Don't do anything to it! Something bad could happen!"

"Yeah right. Like you'd even care if anything bad happened to me."

"You're my responsibility! And we gave Discord a second chance and he came through."

"Wait!? You mean to tell me that the spirit of chaos is walking around Equestria free as a bird?"

"He is a bird! And goat…and dragon…well you get the picture."

"So if I were to become 'good' I could be free too? What if my powers come back?"

Twilight rolled her eyes, "The princesses would stop you. Discord would too."

"Mhhm, sure. Get down from there!" she said as he got up right next to the machine.

"Calm down sweetheart! Nothing bad is gonna happen," he said looking for any opening, and saw a small circle. He pressed it and it popped out making it easy to pull out now.

"Sombra don't!"

He pulled it out and a giant bolt of lighting pushed him back and he started smoking. Everypony looked that way and saw the oval shape starting to hover and take a different shape.

"Sombra!" Twilight said flying over to him. "Are you okay?"

Sombra shook his head, "Yeah. I'm fine. Nothing like getting shocked with ten thousand volts in the morning."

"I told you not to," she said looking at the oval thing. It was spinning around now but it kept taking different shapes.

The Doctor woke up, "AH! What happened!"

He saw the strange figure, "Stop that time machine!" he said getting up. And running towards it. Jack quickly turned around and jumped on it right as it stopped and suddenly disappeared…along with Jack.

"No! I missed it again!" the Doctor said as he hit the floor.

"What just happened!?" McGann said. "Where's Jack!?"

"He was sent to another time period or out in space."

"What!? Will he be alright!?" Kat asked.

"Yes, he can't die. He should be fine," he saw Sombra standing up next to Twilight.

"Oh cool! I'm already in the time period where Sombra turns good! Sorry I always get my time periods messed up."

"He's um…not good yet. We barely found him," Twilight said.

"Gee thanks, and I thought you actually started caring about me now," he said holding his chest.

"After everything you've done? It's gonna take a lot more than almost dyeing for me to care about you."

"Are you sure? You seemed quite worried right now."

"Well I actually care about ponies alright!"

"Guys! Forget I said anything! We need to find Jack and that time machine! I need to see who or what is inside," the Doctor said. "I've followed him for quite some time, but he or she was always a couple of steps ahead of me!"

"How is that possible?" Yumi said.

"Well it is a time machine," ID said. "The only thing I don't get is how all three of us ended up here at the same time?"

"Yes. That's an excellent question," the Doctor said walking back and forth. "You guys must have a way to trace Jack don't you?"

"Well…" Yumi started, "he does have some equipment on, but he is most likely out of range or even in a different time period."

"Alright! Good enough for me! My TARDIS should be able to locate him any time and any place. I need you guys to come with me. Sombra should know a bit about time travel from past experience."

Sombra knew what he was talking about but said, "I've never time traveled before."

"Haha well you know exactly what I mean. Quickly lets go! I need all of you guys," he said leaving the door wide open for them.

The rest of the Torch Wood team went in, including Luna and ID. Luna was thinking several things about Sombra's past right now and was having a small talk with ID. 'Something's not right here Timid.'

'I know. The Doctor says he becomes a really valuable ally but I don't remember too much about Sombra in my history books.'

'We need to watch out for him.'

The only ones left were Twilight and Sombra. Sombra looked at Twilight and smiled, "After you, Princess."

Twilight wasn't buying it. "You're holding something back! Don't think I don't see right through you! What did he mean you had experience with time travel before?"

"I…" Sombra started but was interrupted.

"Hurry up slow pokes! Get in!"

Twilight brushed it off and walked in. Sombra followed her but kept his mouth close. As the door closed the all too familiar sound came out of the TARDIS and then it disappeared into nothingness.

**A bit too long!? Sorry couldn't figure out where to stop! I just couldn't stop writing! Arg! Well hope you enjoyed it, and what did you think Ellen17? Good enough for ya? ;)**


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